| 2004 | Aligning alignments exactly. | John D. Kececioglu, Dean Starrett |
| 2004 | Algorithms for inferring cis-regulatory structures and protein interaction networks. | Richard M. Karp |
| 2004 | Mining protein family specific residue packing patterns from protein structure graphs. | Jun Huan, Wei Wang, Deepak Bandyopadhyay, Jack Snoeyink, Jan F. Prins, Alexander Tropsha |
| 2004 | The Statistical Significance of Max-Gap Clusters. | Rose Hoberman, David Sankoff, Dannie Durand |
| 2004 | Identifying conserved gene clusters in the presence of orthologous groups. | Xin He, Michael H. Goldwasser |
| 2004 | Perfect phylogeny and haplotype assignment. | Eran Halperin, Richard M. Karp |
| 2004 | Simultaneous identification of duplications and lateral transfers. | Michael T. Hallett, Jens Lagergren, Ali Tofigh |
| 2004 | On the Structure of Reconciliations. | Pawel Grecki, Jerzy Tiuryn |
| 2004 | Reconciliation problems for duplication, loss and horizontal gene transfer. | Pawel Grecki |
| 2004 | Modeling and Analysis of Heterogeneous Regulation in Biological Networks. | Irit Gat-Viks, Amos Tanay, Ron Shamir |
| 2004 | RNAi, genome ultrastructure, and other unexpected tales from the analysis of genetic silencing. | Andrew Fire |
| 2004 | Inferring Cis-region Hierarchies from Patterns in Time-Course Gene Expression Data | Vladimir Filkov, Nameeta Y. Shah |
| 2004 | Discovering temporal relations in molecular pathways using protein-protein interactions. | Martin Farach-Colton, Yang Huang, John L. L. Woolford |
| 2004 | From profiles to patterns and back again: a branch and bound algorithm for finding near optimal motif profiles. | Eleazar Eskin |
| 2004 | Protein similarity from knot theory and geometric convolution. | Michael A. Erdmann |
| 2004 | Fifty years of sequence analysis: what have we learned? | Russell F. Doolittle |
| 2004 | Multiple Genome Alignment by Clustering Pairwise Matches. | Jeong-Hyeon Choi, Kwangmin Choi, Hwan-Gue Cho, Sun Kim |
| 2004 | Finding motifs for insufficient number of sequences with strong binding to transcription facto. | Francis Y. L. Chin, Henry C. M. Leung, Siu-Ming Yiu, Tak Wah Lam, Roni Rosenfeld, Wai Wan Tsang, David K. Smith, Y. Jiang |
| 2004 | Multiple organism gene finding by collapsed gibbs sampling. | Sourav Chatterji, Lior Pachter |
| 2004 | Recent advances on the manipulation of single biomolecules. | Carlos Bustamante |
| 2004 | Toward a Phylogenetically Aware Algorithm for Fast DNA Similarity Search. | Jeremy Buhler, Rachel Nordgren |
| 2004 | Conservation of Combinatorial Structures in Evolution Scenarios. | Sverine Brard, Anne Bergeron, Cdric Chauve |
| 2004 | Learning multiple evolutionary pathways from cross-sectional data. | Niko Beerenwinkel, Jrg Rahnenfhrer, Martin Dumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, Thomas Lengauer |
| 2004 | Probabilistic discovery of overlapping cellular processes and their regulation. | Alexis J. Battle, Eran Segal, Daphne Koller |
| 2004 | Interface surfaces for protein-protein complexes. | Yih-En Andrew Ban, Herbert Edelsbrunner, Johannes Rudolph |